Showing papers by "Academy of Sciences of the Czech Republic published in 2009"

Circular dichroism and conformational polymorphism of DNA

Abstract: Here we review studies that provided important information about conformational properties of DNA using circular dichroic (CD) spectroscopy. The conformational properties include the B-family of structures, A-form, Z-form, guanine quadruplexes, cytosine quadruplexes, triplexes and other less characterized structures. CD spectroscopy is extremely sensitive and relatively inexpensive. This fast and simple method can be used at low- as well as high-DNA concentrations and with short- as well as long-DNA molecules. The samples can easily be titrated with various agents to cause conformational isomerizations of DNA. The course of detected CD spectral changes makes possible to distinguish between gradual changes within a single DNA conformation and cooperative isomerizations between discrete structural states. It enables measuring kinetics of the appearance of particular conformers and determination of their thermodynamic parameters. In careful hands, CD spectroscopy is a valuable tool for mapping conformational properties of particular DNA molecules. Due to its numerous advantages, CD spectroscopy significantly participated in all basic conformational findings on DNA.

Alien species in a warmer world: risks and opportunities

Abstract: Climate change and biological invasions are key processes affecting global biodiversity, yet their effects have usually been considered separately. Here, we emphasise that global warming has enabled alien species to expand into regions in which they previously could not survive and reproduce. Based on a review of climate-mediated biological invasions of plants, invertebrates, fishes and birds, we discuss the ways in which climate change influences biological invasions. We emphasise the role of alien species in a more dynamic context of shifting species' ranges and changing communities. Under these circumstances, management practices regarding the occurrence of 'new' species could range from complete eradication to tolerance and even consideration of the 'new' species as an enrichment of local biodiversity and key elements to maintain ecosystem services.

Impact of invasive plants on the species richness, diversity and composition of invaded communities

Abstract: Summary 1. Much attention has been paid to negative effects of alien species on resident communities but studies that quantify community-level effects of a number of invasive plants are scarce. We address this issue by assessing the impact of 13 species invasive in the Czech Republic on a wide range of plant communities. 2. Vegetation in invaded and uninvaded plots with similar site conditions was sampled. All species of vascular plants were recorded, their covers were estimated and used as importance values for calculating the Shannon diversity index H\ evenness J and Sorensen index of similarity between invaded and uninvaded vegetation. 3. With the exception of two invasive species, species richness, diversity and evenness were reduced in invaded plots. Species exhibiting the greatest impact reduced species numbers per plot and the total number of species recorded in the communities sampled by almost 90%. A strong reduction of species number at the plot scale resulted in a marked reduction in the total species number at the landscape scale, and in less similarity between invaded and uninvaded vegetation. The decrease in species richness in invaded compared to uninvaded plots is largely driven by the identity of the invading species, whereas the major determinants of the decrease in Shannon diversity and evenness are the cover and height of invading species, and differences between height and cover of invading and dominant native species, independent of species identity. 4. Synthesis. Management decisions based on impact need to distinguish between invasive species, as their effects on diversity and composition of resident vegetation differ largely. Tall invading species capable of forming populations with the cover markedly greater than that of native dominant species exert the most severe effects on species diversity and evenness. Since a strong impact on the community scale is associated with reduction in species diversity at higher scales, invaders with a high impact represent a serious hazard to the landscape.

Systematic measurements of identified particle spectra in pp, d+Au, and Au+Au collisions at the star detector.

Abstract: Identified charged-particle spectra of pi(+/-), K(+/-), p, and (p) over bar at midrapidity (vertical bar y vertical bar < 0.1) measured by the dE/dx method in the STAR (solenoidal tracker at the BNL Relativistic Heavy Ion Collider) time projection chamber are reported for pp and d + Au collisions at root s(NN) = 200 GeV and for Au + Au collisions at 62.4, 130, and 200 GeV. Average transverse momenta, total particle production, particle yield ratios, strangeness, and baryon production rates are investigated as a function of the collision system and centrality. The transverse momentum spectra are found to be flatter for heavy particles than for light particles in all collision systems; the effect is more prominent for more central collisions. The extracted average transverse momentum of each particle species follows a trend determined by the total charged-particle multiplicity density. The Bjorken energy density estimate is at least several GeV/fm(3) for a formation time less than 1 fm/c. A significantly larger net-baryon density and a stronger increase of the net-baryon density with centrality are found in Au + Au collisions at 62.4 GeV than at the two higher energies. Antibaryon production relative to total particle multiplicity is found to be constant over centrality, but increases with the collision energy. Strangeness production relative to total particle multiplicity is similar at the three measured RHIC energies. Relative strangeness production increases quickly with centrality in peripheral Au + Au collisions, to a value about 50% above the pp value, and remains rather constant in more central collisions. Bulk freeze-out properties are extracted from thermal equilibrium model and hydrodynamics-motivated blast-wave model fits to the data. Resonance decays are found to have little effect on the extracted kinetic freeze-out parameters because of the transverse momentum range of our measurements. The extracted chemical freeze-out temperature is constant, independent of collision system or centrality; its value is close to the predicted phase-transition temperature, suggesting that chemical freeze-out happens in the vicinity of hadronization and the chemical freeze-out temperature is universal despite the vastly different initial conditions in the collision systems. The extracted kinetic freeze-out temperature, while similar to the chemical freeze-out temperature in pp, d + Au, and peripheral Au + Au collisions, drops significantly with centrality in Au + Au collisions, whereas the extracted transverse radial flow velocity increases rapidly with centrality. There appears to be a prolonged period of particle elastic scatterings from chemical to kinetic freeze-out in central Au + Au collisions. The bulk properties extracted at chemical and kinetic freeze-out are observed to evolve smoothly over the measured energy range, collision systems, and collision centralities.

Phytoplankton in the ocean use non-phosphorus lipids in response to phosphorus scarcity.

Abstract: Phosphorus is an obligate requirement for the growth of all organisms; major biochemical reservoirs of phosphorus in marine plankton include nucleic acids and phospholipids. However, eukaryotic phytoplankton and cyanobacteria (that is, 'phytoplankton' collectively) have the ability to decrease their cellular phosphorus content when phosphorus in their environment is scarce. The biochemical mechanisms that allow phytoplankton to limit their phosphorus demand and still maintain growth are largely unknown. Here we show that phytoplankton, in regions of oligotrophic ocean where phosphate is scarce, reduce their cellular phosphorus requirements by substituting non-phosphorus membrane lipids for phospholipids. In the Sargasso Sea, where phosphate concentrations were less than 10 nmol l-1, we found that only 1.3 +/- 0.6% of phosphate uptake was used for phospholipid synthesis; in contrast, in the South Pacific subtropical gyre, where phosphate was greater than 100 nmol l-1, plankton used 17 6% (ref. 6). Examination of the planktonic membrane lipids at these two locations showed that classes of sulphur- and nitrogen-containing membrane lipids, which are devoid of phosphorus, were more abundant in the Sargasso Sea than in the South Pacific. Furthermore, these non-phosphorus, 'substitute lipids' were dominant in phosphorus-limited cultures of all of the phytoplankton species we examined. In contrast, the marine heterotrophic bacteria we examined contained no substitute lipids and only phospholipids. Thus heterotrophic bacteria, which compete with phytoplankton for nutrients in oligotrophic regions like the Sargasso Sea, appear to have a biochemical phosphorus requirement that phytoplankton avoid by using substitute lipids. Our results suggest that phospholipid substitutions are fundamental biochemical mechanisms that allow phytoplankton to maintain growth in the face of phosphorus limitation.

Surface plasmon resonance (SPR) sensors: approaching their limits?

Abstract: We report on a unified theoretical model of the resolution of SPR sensors which makes it possible to predict the ultimate performance of all major configurations of SPR sensors. The theory indicates that the performance of SPR sensors is independent of the method of excitation of surface plasmons (prism or grating coupling) or the method of modulation (amplitude, angular or wavelength) and depends dominantly on the noise properties of the light source and detector. Results of the theoretical analysis are compared with the performance reported for several SPR sensors to illustrate that the best state-of-art SPR sensors are approaching their theoretical limits. Possibilities for further advances in the performance of SPR sensor technology are discussed.

Room-temperature ferromagnetism in graphite driven by two-dimensional networks of point defects

Abstract: Ferromagnetism usually only occurs in materials containing elements that form covalent 3d and 4f bonds. Its occurrence in pure carbon is therefore surprising, even controversial. A systematic magnetic force microscope study indicates that ferromagnetism in graphite is the result of localized spins that arise at grain boundaries.

Azimuthal charged-particle correlations and possible local strong parity violation

Abstract: Parity-odd domains, corresponding to nontrivial topological solutions of the QCD vacuum, might be created during relativistic heavy-ion collisions. These domains are predicted to lead to charge separation of quarks along the system's orbital momentum axis. We investigate a three-particle azimuthal correlator which is a P even observable, but directly sensitive to the charge separation effect. We report measurements of charged hadrons near center-of-mass rapidity with this observable in Au+Au and Cu+Cu collisions at s(NN)=200 GeV using the STAR detector. A signal consistent with several expectations from the theory is detected. We discuss possible contributions from other effects that are not related to parity violation.

A Mouse Speciation Gene Encodes a Meiotic Histone H3 Methyltransferase

Abstract: Speciation genes restrict gene flow between the incipient species and related taxa. Three decades ago, we mapped a mammalian speciation gene, hybrid sterility 1 (Hst1), in the intersubspecific hybrids of house mouse. Here, we identify this gene as Prdm9, encoding a histone H3 lysine 4 trimethyltransferase. We rescued infertility in male hybrids with bacterial artificial chromosomes carrying Prdm9 from a strain with the "fertility" Hst1(f) allele. Sterile hybrids display down-regulated microrchidia 2B (Morc2b) and fail to compartmentalize gammaH2AX into the pachynema sex (XY) body. These defects, seen also in Prdm9-null mutants, are rescued by the Prdm9 transgene. Identification of a vertebrate hybrid sterility gene reveals a role for epigenetics in speciation and opens a window to a hybrid sterility gene network.

Perceptions of aging across 26 cultures and their culture-level associates.

Abstract: College students (N=3,435) in 26 cultures reported their perceptions of age-related changes in physical, cognitive, and socioemotional areas of functioning and rated societal views of aging within their culture. There was widespread cross-cultural consensus regarding the expected direction of aging trajectories with (a) perceived declines in societal views of aging, physical attractiveness, the ability to perform everyday tasks, and new learning; (b) perceived increases in wisdom, knowledge, and received respect; and (c) perceived stability in family authority and life satisfaction. Cross-cultural variations in aging perceptions were associated with culture-level indicators of population aging, education levels, values, and national character stereotypes. These associations were stronger for societal views on aging and perceptions of socioemotional changes than for perceptions of physical and cognitive changes. A consideration of culture-level variables also suggested that previously reported differences in aging perceptions between Asian and Western countries may be related to differences in population structure.

Spectroelectrochemistry: the best of two worlds

Abstract: The combination of reaction-oriented electrochemistry with species-focussed spectroscopy in spectroelectrochemistry (SEC) allows for a more complete analysis of single and multiple electron-transfer processes and redox reactions in general. Practical considerations and guidelines are provided in this tutorial review, and selected examples involving UV-VIS-NIR and IR absorption spectroscopy as well as electron paramagnetic resonance (EPR) are presented to illustrate the potential and the applicability of this technique.

Plant extinctions and introductions lead to phylogenetic and taxonomic homogenization of the European flora

Abstract: Human activities have altered the composition of biotas through two fundamental processes: native extinctions and alien introductions. Both processes affect the taxonomic (i.e., species identity) and phylogenetic (i.e., species evolutionary history) structure of species assemblages. However, it is not known what the relative magnitude of these effects is at large spatial scales. Here we analyze the large-scale effects of plant extinctions and introductions on taxonomic and phylogenetic diversity of floras across Europe, using data from 23 regions. Considering both native losses and alien additions in concert reveals that plant invasions since AD 1500 exceeded extinctions, resulting in (i) increased taxonomic diversity (i.e., species richness) but decreased phylogenetic diversity within European regions, and (ii) increased taxonomic and phylogenetic similarity among European regions. Those extinct species were phylogenetically and taxonomically unique and typical of individual regions, and extinctions usually were not continent-wide and therefore led to differentiation. By contrast, because introduced alien species tended to be closely related to native species, the floristic differentiation due to species extinction was lessened by taxonomic and phylogenetic homogenization effects. This was especially due to species that are alien to a region but native to other parts of Europe. As a result, floras of many European regions have partly lost and will continue to lose their uniqueness. The results suggest that biodiversity needs to be assessed in terms of both species taxonomic and phylogenetic identity, but the latter is rarely used as a metric of the biodiversity dynamics.

Quantum spin Hall effect in a transition metal oxide Na2IrO3.

Abstract: We study theoretically the electronic states in a $5d$ transition metal oxide ${\mathrm{Na}}_{2}{\mathrm{IrO}}_{3}$, in which both the spin-orbit interaction and the electron correlation play crucial roles. A tight-binding model analysis together with the first-principles band structure calculation predicts that this material is a layered quantum spin Hall system. Because of the electron correlation, an antiferromagnetic order first develops at the edge, and later inside the bulk at low temperatures.

Observation of single top-quark production

Abstract: We report observation of the electroweak production of single top quarks in pp collisions at s=1.96 TeV based on 2.3 fb(-1) of data collected by the D0 detector at the Fermilab Tevatron Collider. Using events containing an isolated electron or muon and missing transverse energy, together with jets originating from the fragmentation of b quarks, we measure a cross section of sigma(pp -> tb+X,tqb+X)=3.94 +/- 0.88 pb. The probability to measure a cross section at this value or higher in the absence of signal is 2.5x10(-7), corresponding to a 5.0 standard deviation significance for the observation.

The impact and recovery of asteroid 2008 TC 3

Abstract: On 6 October 2008, a small Earth-bound asteroid designated 2008 TC3 was discovered by the Catalina Sky Survey. Some 19 hours — and many astronomical observations — later it entered the atmosphere and disintegrated at 37 km altitude. No macroscopic fragments were expected to have survived but a dedicated search along the approach trajectory in a desert in northern Sudan has recovered 47 meteorites, fragments of a single body named Almahata Sitta, with a total mass of 3.95 kg. The asteroid and meteorite reflectance spectra identify the asteroid as surface matter from a class 'F' asteroid, material so fragile that it was not previously represented in meteorite collections. To have recovered meteorites from a known class of asteroids is a coup on a par with a successful spacecraft sample-return mission — without the rocket science. On 6 October 2008, a small asteroid designated 2008 TC3 hit the Earth in northern Sudan. Jenniskens et al. searched along the approach trajectory and luckily found 47 bits of a meteorite named Almahata Sitta. Analysis reveals it to be a porous achondrite and a polymict ureilite, and so the asteroid was F-class (dark carbon-rich anomalous ureilites). In the absence of a firm link between individual meteorites and their asteroidal parent bodies, asteroids are typically characterized only by their light reflection properties, and grouped accordingly into classes1,2,3. On 6 October 2008, a small asteroid was discovered with a flat reflectance spectrum in the 554–995 nm wavelength range, and designated 2008 TC3 (refs 4–6). It subsequently hit the Earth. Because it exploded at 37 km altitude, no macroscopic fragments were expected to survive. Here we report that a dedicated search along the approach trajectory recovered 47 meteorites, fragments of a single body named Almahata Sitta, with a total mass of 3.95 kg. Analysis of one of these meteorites shows it to be an achondrite, a polymict ureilite, anomalous in its class: ultra-fine-grained and porous, with large carbonaceous grains. The combined asteroid and meteorite reflectance spectra identify the asteroid as F class3, now firmly linked to dark carbon-rich anomalous ureilites, a material so fragile it was not previously represented in meteorite collections.

Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes.

Abstract: Because of its construction and parametrization for more than 80 elements, the semiempirical quantum chemical PM6 method is superior to other similar methods. Despite its advantages, however, the PM6 method fails for the description of noncovalent interactions, specifically the dispersion energy and H-bonding. Upon inclusion of correction terms for dispersion and H-bonding, the performance of the method was found to be dramatically improved. The former correction included two parameters in the damping function that were parametrized to reproduce the benchmark interaction energies [CCSD(T)/complete basis set (CBS) limit] of the dispersion-bonded complexes from the S22 data set. The latter correction was parametrized on an extended set of H-bonded stabilization energies determined at the MP2/cc-pVTZ level. The resulting PM6-DH method was tested on the S22 data set, for which chemical accuracy (error < 1 kcal/mol) was achieved, and also on the JSCH2005 set, for which significant improvement over the original...

Will Threat of Biological Invasions Unite the European Union

Abstract: New data on the extent of biological invasions pose major regulatory and political challenges to European institutions.

Br···O Complexes as Probes of Factors Affecting Halogen Bonding: Interactions of Bromobenzenes and Bromopyrimidines with Acetone

Abstract: Halogen bonding is a unique type of noncovalent binding phenomenon in which a halogen atom interacts attractively with an electronegative atom such as oxygen or nitrogen. These types of interactions have been the subject of many recent investigations because of their potential in the development of new materials and pharmaceutical compounds. Recently, it was observed that most halogen bonding interactions in biological contexts involve close contacts between a halogen bound to an aromatic ring and a carbonyl oxygen on a protein’s backbone structure. In this work we investigate interactions of substituted bromobenzenes and bromopyrimidines with acetone to ascertain the effects of various substituents upon the strengths of these interactions. It was found that replacement of ring hydrogens in these systems has dramatic effects upon the interaction strengths of the resulting complexes, which have interaction energies between −1.80 and −7.11 kcal/mol. Examination of the electrostatic potentials of the substit...

CpG methylation controls reactivation of HIV from latency.

Abstract: DNA methylation of retroviral promoters and enhancers localized in the provirus 5' long terminal repeat (LTR) is considered to be a mechanism of transcriptional suppression that allows retroviruses to evade host immune responses and antiretroviral drugs. However, the role of DNA methylation in the control of HIV-1 latency has never been unambiguously demonstrated, in contrast to the apparent importance of transcriptional interference and chromatin structure, and has never been studied in HIV-1-infected patients. Here, we show in an in vitro model of reactivable latency and in a latent reservoir of HIV-1-infected patients that CpG methylation of the HIV-1 5' LTR is an additional epigenetic restriction mechanism, which controls resistance of latent HIV-1 to reactivation signals and thus determines the stability of the HIV-1 latency. CpG methylation acts as a late event during establishment of HIV-1 latency and is not required for the initial provirus silencing. Indeed, the latent reservoir of some aviremic patients contained high proportions of the non-methylated 5' LTR. The latency controlled solely by transcriptional interference and by chromatin-dependent mechanisms in the absence of significant promoter DNA methylation tends to be leaky and easily reactivable. In the latent reservoir of HIV-1-infected individuals without detectable plasma viremia, we found HIV-1 promoters and enhancers to be hypermethylated and resistant to reactivation, as opposed to the hypomethylated 5' LTR in viremic patients. However, even dense methylation of the HIV-1 5'LTR did not confer complete resistance to reactivation of latent HIV-1 with some histone deacetylase inhibitors, protein kinase C agonists, TNF-alpha, and their combinations with 5-aza-2deoxycytidine: the densely methylated HIV-1 promoter was most efficiently reactivated in virtual absence of T cell activation by suberoylanilide hydroxamic acid. Tight but incomplete control of HIV-1 latency by CpG methylation might have important implications for strategies aimed at eradicating HIV-1 infection.

The high-acceptance dielectron spectrometer HADES

Abstract: HADES is a versatile magnetic spectrometer aimed at studying dielectron production in pion, proton and heavy-ion-induced collisions. Its main features include a ring imaging gas Cherenkov detector for electron-hadron discrimination, a tracking system consisting of a set of 6 superconducting coils producing a toroidal field and drift chambers and a multiplicity and electron trigger array for additional electron-hadron discrimination and event characterization. A two-stage trigger system enhances events containing electrons. The physics program is focused on the investigation of hadron properties in nuclei and in the hot and dense hadronic matter. The detector system is characterized by an 85% azimuthal coverage over a polar angle interval from 18° to 85°, a single electron efficiency of 50% and a vector meson mass resolution of 2.5%. Identification of pions, kaons and protons is achieved combining time-of-flight and energy loss measurements over a large momentum range (0.1 < p < 1.0 GeV/c). This paper describes the main features and the performance of the detector system. © Societa Italiana di Fisica / Springer-Verlag 2009.